A handy program I use to analyze MRI data is called FSL. “FSL is a comprehensive library of image analysis and statistical tools for FMRI, MRI and DTI brain imaging data. FSL is written mainly by members of the Analysis Group, FMRIB, Oxford, UK” (from the FSL website). It is powerful, flexible, and well-maintained. There is a very active community listserv too.
All of my research is structural MRI-based, so the main FSL tools I use are: Brain Extraction tool (BET), SUSAN (which reduces noise nonlinearly), FAST (an automated segmentation program that can separate the MR images into different tissue types), FLIRT (a linear registration program), and FUGUE (a program that can unwarp the MR images; there is often distortion in MRIs caused at scan acquisition by head movements or other problems).
I’ve been very pleased with the software so far. It’s free software and available to pretty much anyone for use. I have no affiliation with the software developers, I am just a pleased user of the software. I would post some of the images I’ve processed with FSL, however, due to IRB, HIPPA, and confidentiality limitations, I am unable to.